From 3fd533c8fdedc7a6761911c3011e031568d0d7b8 Mon Sep 17 00:00:00 2001
From: "Aaron A. King" <kingaa@umich.edu>
Date: Mon, 12 Feb 2024 11:06:47 -0500
Subject: [PATCH] change parameter name

---
 DESCRIPTION             |  4 ++--
 R/seir.R                | 16 ++++++++--------
 R/si2r.R                | 10 +++++-----
 R/siir.R                | 10 +++++-----
 R/sir.R                 | 16 ++++++++--------
 examples/movie.R        |  2 +-
 examples/seir.R         |  4 ++--
 examples/si2r.R         |  2 +-
 examples/sir.R          |  4 ++--
 man/seir.Rd             | 12 ++++++------
 man/si2r.Rd             |  8 ++++----
 man/siir.Rd             |  6 +++---
 man/sir.Rd              | 20 ++++++++++----------
 man/treeplot.Rd         |  2 +-
 src/seir.cc             |  8 ++++----
 src/seirs_pomp.cc       |  4 ++--
 src/si2r.cc             |  8 ++++----
 src/siir.cc             |  8 ++++----
 src/sir.cc              |  8 ++++----
 src/sirs_pomp.c         |  6 +++---
 tests/curtail.R         |  2 +-
 tests/curtail.Rout.save |  2 +-
 tests/diagram.R         | 10 +++++-----
 tests/diagram.Rout.save | 12 ++++++------
 tests/seir1.R           |  6 +++---
 tests/seir1.Rout.save   |  6 +++---
 tests/seir2.R           |  6 +++---
 tests/seir2.Rout.save   |  6 +++---
 tests/si2r.R            |  2 +-
 tests/si2r.Rout.save    |  2 +-
 tests/sir1.R            |  6 +++---
 tests/sir1.Rout.save    |  6 +++---
 yaml/R/seir.R           | 10 +++++-----
 yaml/R/si2r.R           | 10 +++++-----
 yaml/R/siir.R           | 10 +++++-----
 yaml/R/sir.R            | 10 +++++-----
 yaml/seir.yml           |  6 +++---
 yaml/si2r.yml           |  6 +++---
 yaml/siir.yml           |  6 +++---
 yaml/sir.yml            |  6 +++---
 yaml/src/seir.cc        |  8 ++++----
 yaml/src/si2r.cc        |  8 ++++----
 yaml/src/siir.cc        |  8 ++++----
 yaml/src/sir.cc         |  8 ++++----
 44 files changed, 160 insertions(+), 160 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c3d78c1..62a675a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
-Version: 0.10.1.5
-Date: 2024-01-27
+Version: 0.10.2.0
+Date: 2024-02-12
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu",comment=c(ORCID="0000-0001-6159-3207")),
 	  person(given=c("Qianying"),family="Lin",role=c("aut"),comment=c(ORCID="0000-0001-8620-9910"))
 	  )
diff --git a/R/seir.R b/R/seir.R
index e284e0f..86556b2 100644
--- a/R/seir.R
+++ b/R/seir.R
@@ -10,7 +10,7 @@
 ##' @param sigma progression rate
 ##' @param gamma recovery rate
 ##' @param psi per capita sampling rate
-##' @param delta rate of waning of immunity
+##' @param omega rate of waning of immunity
 ##' @param S0 initial size of susceptible population
 ##' @param E0 initial size of exposed population
 ##' @param I0 initial size of infected population
@@ -26,9 +26,9 @@ NULL
 ##' @export
 runSEIR <- function (
   time, t0 = 0,
-  Beta = 4, sigma = 1, gamma = 1, psi = 1, delta = 0, S0 = 100, E0 = 5, I0 = 5, R0 = 0
+  Beta = 4, sigma = 1, gamma = 1, psi = 1, omega = 0, S0 = 100, E0 = 5, I0 = 5, R0 = 0
 ) {
-  params <- c(Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,delta=delta)
+  params <- c(Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,omega=omega)
   ivps <- c(S0=S0,E0=E0,I0=I0,R0=R0)
   if (any(ivps < 0))
     pStop(paste(sQuote(names(ivps)),collapse=","),
@@ -43,10 +43,10 @@ runSEIR <- function (
 ##' @export
 continueSEIR <- function (
   object, time,
-  Beta = NA, sigma = NA, gamma = NA, psi = NA, delta = NA
+  Beta = NA, sigma = NA, gamma = NA, psi = NA, omega = NA
 ) {
   params <- c(
-    Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,delta=delta
+    Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,omega=omega
   )
   x <- .Call(P_reviveSEIR,object,params)
   .Call(P_runSEIR,x,time) |>
@@ -63,7 +63,7 @@ continueSEIR <- function (
 ##' @export
 seirs_pomp <- function (
   x,
-  Beta, sigma, gamma, psi, delta = 0,
+  Beta, sigma, gamma, psi, omega = 0,
   S0, E0, I0, R0
 )
 {
@@ -84,7 +84,7 @@ seirs_pomp <- function (
     t0=dat$time[1L],
     times=dat$time[-1L],
     params=c(
-      Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,delta=delta,
+      Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,omega=omega,
       ic,N=sum(ic)
     ),
     nstatevars=nsample+8L,
@@ -95,7 +95,7 @@ seirs_pomp <- function (
     dmeasure="seirs_dmeas",
     statenames=c("S","E","I","R","ll","node","linE","linI","lineage"),
     paramnames=c(
-      "Beta","sigma","gamma","psi","delta",
+      "Beta","sigma","gamma","psi","omega",
       "S0","E0","I0","R0","N"
     ),
     PACKAGE="phylopomp"
diff --git a/R/si2r.R b/R/si2r.R
index 40667a0..ea2918e 100644
--- a/R/si2r.R
+++ b/R/si2r.R
@@ -11,7 +11,7 @@
 ##' @param Beta transmission rate
 ##' @param mu mean superspreading-event cluster size
 ##' @param gamma recovery rate
-##' @param delta rate of waning of immunity
+##' @param omega rate of waning of immunity
 ##' @param psi1,psi2 sampling rates for demes 1 and 2, respectively
 ##' @param sigma12,sigma21 movement rates from deme 1 to 2 and 2 to 1, respectively
 ##' @param S0 initial size of susceptible population
@@ -37,13 +37,13 @@ NULL
 ##' @export
 runSI2R <- function (
   time, t0 = 0,
-  Beta = 5, mu = 5, gamma = 1, delta = 0,
+  Beta = 5, mu = 5, gamma = 1, omega = 0,
   psi1 = 1, psi2 = 0,
   sigma12 = 1, sigma21 = 3,
   S0 = 500, I0 = 10, R0 = 0
 ) {
   params <- c(
-    Beta=Beta,mu=mu,gamma=gamma,delta=delta,
+    Beta=Beta,mu=mu,gamma=gamma,omega=omega,
     psi1=psi1,psi2=psi2,
     sigma12=sigma12,sigma21=sigma21
   )
@@ -58,12 +58,12 @@ runSI2R <- function (
 ##' @export
 continueSI2R <- function (
   object, time,
-  Beta = NA, mu = NA, gamma = NA, delta = NA,
+  Beta = NA, mu = NA, gamma = NA, omega = NA,
   psi1 = NA, psi2 = NA,
   sigma12 = NA, sigma21 = NA
 ) {
   params <- c(
-    Beta=Beta,mu=mu,gamma=gamma,delta=delta,
+    Beta=Beta,mu=mu,gamma=gamma,omega=omega,
     psi1=psi1,psi2=psi2,
     sigma12=sigma12,sigma21=sigma21
   )
diff --git a/R/siir.R b/R/siir.R
index 365a5c3..408ce89 100644
--- a/R/siir.R
+++ b/R/siir.R
@@ -13,7 +13,7 @@
 ##' @param gamma recovery rate.
 ##' @param psi1,psi2 sampling rates.
 ##' @param sigma12,sigma21 movement rates from deme 1 to 2 and 2 to 1, respectively
-##' @param delta rate of loss of immunity
+##' @param omega rate of loss of immunity
 ##' @param S0 initial size of susceptible population.
 ##' @param I1_0 initial size of I2 population.
 ##' @param I2_0 initial size of I2 population.
@@ -31,10 +31,10 @@ runSIIR <- function (
   Beta1 = 5, Beta2 = 5, gamma = 1,
   psi1 = 1, psi2 = 0,
   sigma12 = 0, sigma21 = 0,
-  delta = 0,
+  omega = 0,
   S0 = 500, I1_0 = 10, I2_0 = 10, R0 = 0
 ) {
-  params <- c(Beta1=Beta1,Beta2=Beta2,gamma=gamma,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21,delta=delta)
+  params <- c(Beta1=Beta1,Beta2=Beta2,gamma=gamma,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21,omega=omega)
   ivps <- c(S0=S0,I1_0=I1_0,I2_0=I2_0,R0=R0)
   x <- .Call(P_makeSIIR,params,ivps,t0)
   .Call(P_runSIIR,x,time) |>
@@ -48,10 +48,10 @@ continueSIIR <- function (
   Beta1 = NA, Beta2 = NA, gamma = NA,
   psi1 = NA, psi2 = NA,
   sigma12 = NA, sigma21 = NA,
-  delta = NA
+  omega = NA
 ) {
   params <- c(
-    Beta1=Beta1,Beta2=Beta2,gamma=gamma,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21,delta=delta
+    Beta1=Beta1,Beta2=Beta2,gamma=gamma,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21,omega=omega
   )
   x <- .Call(P_reviveSIIR,object,params)
   .Call(P_runSIIR,x,time) |>
diff --git a/R/sir.R b/R/sir.R
index 422e833..f439748 100644
--- a/R/sir.R
+++ b/R/sir.R
@@ -9,7 +9,7 @@
 ##' @param Beta transmission rate.
 ##' @param gamma recovery rate.
 ##' @param psi sampling rate.
-##' @param delta immunity waning rate
+##' @param omega immunity waning rate
 ##' @param S0 initial size of susceptible population.
 ##' @param I0 initial size of infected population.
 ##' @param R0 initial size of recovered population.
@@ -24,10 +24,10 @@ NULL
 ##' @export
 runSIR <- function (
   time,  t0 = 0,
-  Beta = 2, gamma = 1, psi = 1, delta = 0,
+  Beta = 2, gamma = 1, psi = 1, omega = 0,
   S0 = 100, I0 = 2, R0 = 0
 ) {
-  params <- c(Beta=Beta,gamma=gamma,psi=psi,delta=delta)
+  params <- c(Beta=Beta,gamma=gamma,psi=psi,omega=omega)
   ivps <- c(S0=S0,I0=I0,R0=R0)
   if (any(ivps < 0))
     pStop(paste(sQuote(names(ivps)),collapse=","),
@@ -45,9 +45,9 @@ runSIRS <- runSIR
 ##' @inheritParams simulate
 ##' @export
 continueSIR <- function (
-  object, time, Beta = NA, gamma = NA, psi = NA, delta = NA
+  object, time, Beta = NA, gamma = NA, psi = NA, omega = NA
 ) {
-  params <- c(Beta=Beta,gamma=gamma,psi=psi,delta=delta)
+  params <- c(Beta=Beta,gamma=gamma,psi=psi,omega=omega)
   x <- .Call(P_reviveSIR,object,params)
   .Call(P_runSIR,x,time) |>
     structure(model="SIR",class=c("gpsim","gpgen"))
@@ -61,7 +61,7 @@ continueSIR <- function (
 ##' \code{sir_pomp} constructs a \pkg{pomp} object containing a given set of data and a SIR model.
 ##' @importFrom pomp pomp onestep covariate_table
 ##' @export
-sir_pomp <- function (x, Beta, gamma, psi, delta = 0, S0, I0, R0, t0=0)
+sir_pomp <- function (x, Beta, gamma, psi, omega = 0, S0, I0, R0, t0=0)
 {
   ic <- as.integer(c(S0,I0,R0))
   names(ic) <- c("S0","I0","R0")
@@ -74,7 +74,7 @@ sir_pomp <- function (x, Beta, gamma, psi, delta = 0, S0, I0, R0, t0=0)
   pomp(
     data=NULL,
     times=dat$time[-1L],t0=t0,
-    params=c(Beta=Beta,gamma=gamma,psi=psi,delta=delta,ic,N=sum(ic)),
+    params=c(Beta=Beta,gamma=gamma,psi=psi,omega=omega,ic,N=sum(ic)),
     covar=covariate_table(
       dat,
       times="time",
@@ -84,7 +84,7 @@ sir_pomp <- function (x, Beta, gamma, psi, delta = 0, S0, I0, R0, t0=0)
     rprocess=onestep("sirs_gill"),
     dmeasure="sirs_dmeas",
     statenames=c("S","I","R","ll"),
-    paramnames=c("Beta","gamma","psi","delta","S0","I0","R0","N"),
+    paramnames=c("Beta","gamma","psi","omega","S0","I0","R0","N"),
     covarnames=c("lineages","code"),
     PACKAGE="phylopomp"
   )
diff --git a/examples/movie.R b/examples/movie.R
index 817462a..8cac940 100644
--- a/examples/movie.R
+++ b/examples/movie.R
@@ -8,7 +8,7 @@
   )
 
   pb <- utils::txtProgressBar(0,length(times),0,style=3)
-  x <- simulate("SIIR",time=0,Beta1=5,Beta2=10,gamma=1,delta=0.5,
+  x <- simulate("SIIR",time=0,Beta1=5,Beta2=10,gamma=1,omega=0.5,
     psi1=0.2,psi2=0.1,sigma12=1,sigma21=1,S0=200,I1_0=3,I2_0=2)
   for (k in seq_len(length(times))) {
     x <- simulate(x,time=times[k])
diff --git a/examples/seir.R b/examples/seir.R
index 8e8c70a..1eccdc4 100644
--- a/examples/seir.R
+++ b/examples/seir.R
@@ -9,8 +9,8 @@ runSEIR(Beta=3,gamma=0.1,psi=0.2,S0=100,I0=5,R0=0,time=2,t0=0) -> x
 plot_grid(plotlist=list(plot(x,points=TRUE),diagram(x)),
   ncol=1,rel_heights=c(4,1))
 
-simulate("SEIR",sigma=1,delta=1,time=20,I0=4) |> plot(obscure=FALSE)
+simulate("SEIR",sigma=1,omega=1,time=20,I0=4) |> plot(obscure=FALSE)
 
-simulate("SEIR",sigma=1,delta=1,time=20,I0=4) |>
+simulate("SEIR",sigma=1,omega=1,time=20,I0=4) |>
   lineages(obscure=FALSE) |>
   plot()
diff --git a/examples/si2r.R b/examples/si2r.R
index 10ff52a..88ef708 100644
--- a/examples/si2r.R
+++ b/examples/si2r.R
@@ -12,7 +12,7 @@ simulate("SI2R",time=5) |>
 simulate("SI2R",time=2) |>
   diagram(m=30)
 
-simulate("SI2R",time=20,delta=0.2,mu=20) -> x
+simulate("SI2R",time=20,omega=0.2,mu=20) -> x
 plot_grid(
   x |> plot(obscure=FALSE),
   x |> lineages(obscure=FALSE) |> plot(),
diff --git a/examples/sir.R b/examples/sir.R
index 8c8017f..ab64f16 100644
--- a/examples/sir.R
+++ b/examples/sir.R
@@ -9,5 +9,5 @@ runSIR(Beta=3,gamma=0.1,psi=0.2,S0=100,I0=5,R0=0,time=2,t0=0) -> x
 plot_grid(plotlist=list(plot(x,points=TRUE),diagram(x)),
   ncol=1,rel_heights=c(4,1))
 
-simulate("SIRS",delta=1,time=20,I0=4) |> plot()
-simulate("SIRS",delta=1,time=20,I0=4) |> lineages() |> plot()
+simulate("SIRS",omega=1,time=20,I0=4) |> plot()
+simulate("SIRS",omega=1,time=20,I0=4) |> lineages() |> plot()
diff --git a/man/seir.Rd b/man/seir.Rd
index fac223e..f289883 100644
--- a/man/seir.Rd
+++ b/man/seir.Rd
@@ -15,7 +15,7 @@ runSEIR(
   sigma = 1,
   gamma = 1,
   psi = 1,
-  delta = 0,
+  omega = 0,
   S0 = 100,
   E0 = 5,
   I0 = 5,
@@ -29,10 +29,10 @@ continueSEIR(
   sigma = NA,
   gamma = NA,
   psi = NA,
-  delta = NA
+  omega = NA
 )
 
-seirs_pomp(x, Beta, sigma, gamma, psi, delta = 0, S0, E0, I0, R0)
+seirs_pomp(x, Beta, sigma, gamma, psi, omega = 0, S0, E0, I0, R0)
 }
 \arguments{
 \item{time}{final time}
@@ -47,7 +47,7 @@ seirs_pomp(x, Beta, sigma, gamma, psi, delta = 0, S0, E0, I0, R0)
 
 \item{psi}{per capita sampling rate}
 
-\item{delta}{rate of waning of immunity}
+\item{omega}{rate of waning of immunity}
 
 \item{S0}{initial size of susceptible population}
 
@@ -83,9 +83,9 @@ runSEIR(Beta=3,gamma=0.1,psi=0.2,S0=100,I0=5,R0=0,time=2,t0=0) -> x
 plot_grid(plotlist=list(plot(x,points=TRUE),diagram(x)),
   ncol=1,rel_heights=c(4,1))
 
-simulate("SEIR",sigma=1,delta=1,time=20,I0=4) |> plot(obscure=FALSE)
+simulate("SEIR",sigma=1,omega=1,time=20,I0=4) |> plot(obscure=FALSE)
 
-simulate("SEIR",sigma=1,delta=1,time=20,I0=4) |>
+simulate("SEIR",sigma=1,omega=1,time=20,I0=4) |>
   lineages(obscure=FALSE) |>
   plot()
 }
diff --git a/man/si2r.Rd b/man/si2r.Rd
index 47fbb0c..48a71b6 100644
--- a/man/si2r.Rd
+++ b/man/si2r.Rd
@@ -13,7 +13,7 @@ runSI2R(
   Beta = 5,
   mu = 5,
   gamma = 1,
-  delta = 0,
+  omega = 0,
   psi1 = 1,
   psi2 = 0,
   sigma12 = 1,
@@ -29,7 +29,7 @@ continueSI2R(
   Beta = NA,
   mu = NA,
   gamma = NA,
-  delta = NA,
+  omega = NA,
   psi1 = NA,
   psi2 = NA,
   sigma12 = NA,
@@ -47,7 +47,7 @@ continueSI2R(
 
 \item{gamma}{recovery rate}
 
-\item{delta}{rate of waning of immunity}
+\item{omega}{rate of waning of immunity}
 
 \item{psi1, psi2}{sampling rates for demes 1 and 2, respectively}
 
@@ -96,7 +96,7 @@ simulate("SI2R",time=5) |>
 simulate("SI2R",time=2) |>
   diagram(m=30)
 
-simulate("SI2R",time=20,delta=0.2,mu=20) -> x
+simulate("SI2R",time=20,omega=0.2,mu=20) -> x
 plot_grid(
   x |> plot(obscure=FALSE),
   x |> lineages(obscure=FALSE) |> plot(),
diff --git a/man/siir.Rd b/man/siir.Rd
index 36fdc31..891c135 100644
--- a/man/siir.Rd
+++ b/man/siir.Rd
@@ -17,7 +17,7 @@ runSIIR(
   psi2 = 0,
   sigma12 = 0,
   sigma21 = 0,
-  delta = 0,
+  omega = 0,
   S0 = 500,
   I1_0 = 10,
   I2_0 = 10,
@@ -34,7 +34,7 @@ continueSIIR(
   psi2 = NA,
   sigma12 = NA,
   sigma21 = NA,
-  delta = NA
+  omega = NA
 )
 }
 \arguments{
@@ -50,7 +50,7 @@ continueSIIR(
 
 \item{sigma12, sigma21}{movement rates from deme 1 to 2 and 2 to 1, respectively}
 
-\item{delta}{rate of loss of immunity}
+\item{omega}{rate of loss of immunity}
 
 \item{S0}{initial size of susceptible population.}
 
diff --git a/man/sir.Rd b/man/sir.Rd
index 83158b2..2ec64f2 100644
--- a/man/sir.Rd
+++ b/man/sir.Rd
@@ -18,7 +18,7 @@ runSIR(
   Beta = 2,
   gamma = 1,
   psi = 1,
-  delta = 0,
+  omega = 0,
   S0 = 100,
   I0 = 2,
   R0 = 0
@@ -30,15 +30,15 @@ runSIRS(
   Beta = 2,
   gamma = 1,
   psi = 1,
-  delta = 0,
+  omega = 0,
   S0 = 100,
   I0 = 2,
   R0 = 0
 )
 
-continueSIR(object, time, Beta = NA, gamma = NA, psi = NA, delta = NA)
+continueSIR(object, time, Beta = NA, gamma = NA, psi = NA, omega = NA)
 
-sir_pomp(x, Beta, gamma, psi, delta = 0, S0, I0, R0, t0 = 0)
+sir_pomp(x, Beta, gamma, psi, omega = 0, S0, I0, R0, t0 = 0)
 
 runSIRS(
   time,
@@ -46,15 +46,15 @@ runSIRS(
   Beta = 2,
   gamma = 1,
   psi = 1,
-  delta = 0,
+  omega = 0,
   S0 = 100,
   I0 = 2,
   R0 = 0
 )
 
-continueSIRS(object, time, Beta = NA, gamma = NA, psi = NA, delta = NA)
+continueSIRS(object, time, Beta = NA, gamma = NA, psi = NA, omega = NA)
 
-sirs_pomp(x, Beta, gamma, psi, delta = 0, S0, I0, R0, t0 = 0)
+sirs_pomp(x, Beta, gamma, psi, omega = 0, S0, I0, R0, t0 = 0)
 }
 \arguments{
 \item{time}{final time}
@@ -67,7 +67,7 @@ sirs_pomp(x, Beta, gamma, psi, delta = 0, S0, I0, R0, t0 = 0)
 
 \item{psi}{sampling rate.}
 
-\item{delta}{immunity waning rate}
+\item{omega}{immunity waning rate}
 
 \item{S0}{initial size of susceptible population.}
 
@@ -101,8 +101,8 @@ runSIR(Beta=3,gamma=0.1,psi=0.2,S0=100,I0=5,R0=0,time=2,t0=0) -> x
 plot_grid(plotlist=list(plot(x,points=TRUE),diagram(x)),
   ncol=1,rel_heights=c(4,1))
 
-simulate("SIRS",delta=1,time=20,I0=4) |> plot()
-simulate("SIRS",delta=1,time=20,I0=4) |> lineages() |> plot()
+simulate("SIRS",omega=1,time=20,I0=4) |> plot()
+simulate("SIRS",omega=1,time=20,I0=4) |> lineages() |> plot()
 }
 \seealso{
 More example genealogy processes: 
diff --git a/man/treeplot.Rd b/man/treeplot.Rd
index d2cd2b7..8f1222d 100644
--- a/man/treeplot.Rd
+++ b/man/treeplot.Rd
@@ -59,7 +59,7 @@ Plots a genealogical tree.
   )
 
   pb <- utils::txtProgressBar(0,length(times),0,style=3)
-  x <- simulate("SIIR",time=0,Beta1=5,Beta2=10,gamma=1,delta=0.5,
+  x <- simulate("SIIR",time=0,Beta1=5,Beta2=10,gamma=1,omega=0.5,
     psi1=0.2,psi2=0.1,sigma12=1,sigma21=1,S0=200,I1_0=3,I2_0=2)
   for (k in seq_len(length(times))) {
     x <- simulate(x,time=times[k])
diff --git a/src/seir.cc b/src/seir.cc
index 509e1e9..7fe4b09 100644
--- a/src/seir.cc
+++ b/src/seir.cc
@@ -18,7 +18,7 @@ typedef struct {
   double sigma;
   double gamma;
   double psi;
-  double delta;
+  double omega;
   int S0;
   int E0;
   int I0;
@@ -36,7 +36,7 @@ std::string seir_proc_t::yaml (std::string tab) const {
     + YAML_PARAM(sigma)
     + YAML_PARAM(gamma)
     + YAML_PARAM(psi)
-    + YAML_PARAM(delta)
+    + YAML_PARAM(omega)
     + YAML_PARAM(S0)
     + YAML_PARAM(E0)
     + YAML_PARAM(I0)
@@ -57,7 +57,7 @@ void seir_proc_t::update_params (double *p, int n) {
   PARAM_SET(sigma);
   PARAM_SET(gamma);
   PARAM_SET(psi);
-  PARAM_SET(delta);
+  PARAM_SET(omega);
   if (m != n) err("wrong number of parameters!");
 }
 
@@ -79,7 +79,7 @@ double seir_proc_t::event_rates (double *rate, int n) const {
   RATE_CALC(params.sigma * state.E);
   RATE_CALC(params.gamma * state.I);
   RATE_CALC(params.psi * state.I);
-  RATE_CALC(params.delta * state.R);
+  RATE_CALC(params.omega * state.R);
   if (m != n) err("wrong number of events!");
   return total;
 }
diff --git a/src/seirs_pomp.cc b/src/seirs_pomp.cc
index f496f83..8941db9 100644
--- a/src/seirs_pomp.cc
+++ b/src/seirs_pomp.cc
@@ -34,7 +34,7 @@ static void check_lineages
 #define sigma     (__p[__parindex[1]])
 #define gamma     (__p[__parindex[2]])
 #define psi       (__p[__parindex[3]])
-#define Delta     (__p[__parindex[4]])
+#define omega     (__p[__parindex[4]])
 #define S0        (__p[__parindex[5]])
 #define E0        (__p[__parindex[6]])
 #define I0        (__p[__parindex[7]])
@@ -79,7 +79,7 @@ static double event_rates
   }
   rate++;
   // waning
-  event_rate += (*rate = Delta*R);
+  event_rate += (*rate = omega*R);
   rate++;
   // sampling
   *penalty += psi*I;
diff --git a/src/si2r.cc b/src/si2r.cc
index ae77f96..7bacd76 100644
--- a/src/si2r.cc
+++ b/src/si2r.cc
@@ -17,7 +17,7 @@ typedef struct {
   double Beta;
   double mu;
   double gamma;
-  double delta;
+  double omega;
   double psi1;
   double psi2;
   double sigma12;
@@ -37,7 +37,7 @@ std::string si2r_proc_t::yaml (std::string tab) const {
     + YAML_PARAM(Beta)
     + YAML_PARAM(mu)
     + YAML_PARAM(gamma)
-    + YAML_PARAM(delta)
+    + YAML_PARAM(omega)
     + YAML_PARAM(psi1)
     + YAML_PARAM(psi2)
     + YAML_PARAM(sigma12)
@@ -60,7 +60,7 @@ void si2r_proc_t::update_params (double *p, int n) {
   PARAM_SET(Beta);
   PARAM_SET(mu);
   PARAM_SET(gamma);
-  PARAM_SET(delta);
+  PARAM_SET(omega);
   PARAM_SET(psi1);
   PARAM_SET(psi2);
   PARAM_SET(sigma12);
@@ -89,7 +89,7 @@ double si2r_proc_t::event_rates (double *rate, int n) const {
   RATE_CALC(params.psi2 * state.I2);
   RATE_CALC(params.sigma12 * state.I1);
   RATE_CALC(params.sigma21 * state.I2);
-  RATE_CALC(params.delta * state.R);
+  RATE_CALC(params.omega * state.R);
   if (m != n) err("wrong number of events!");
   return total;
 }
diff --git a/src/siir.cc b/src/siir.cc
index b2b2c0c..fa82263 100644
--- a/src/siir.cc
+++ b/src/siir.cc
@@ -21,7 +21,7 @@ typedef struct {
   double psi2;
   double sigma12;
   double sigma21;
-  double delta;
+  double omega;
   int S0;
   int I1_0;
   int I2_0;
@@ -42,7 +42,7 @@ std::string siir_proc_t::yaml (std::string tab) const {
     + YAML_PARAM(psi2)
     + YAML_PARAM(sigma12)
     + YAML_PARAM(sigma21)
-    + YAML_PARAM(delta)
+    + YAML_PARAM(omega)
     + YAML_PARAM(S0)
     + YAML_PARAM(I1_0)
     + YAML_PARAM(I2_0)
@@ -66,7 +66,7 @@ void siir_proc_t::update_params (double *p, int n) {
   PARAM_SET(psi2);
   PARAM_SET(sigma12);
   PARAM_SET(sigma21);
-  PARAM_SET(delta);
+  PARAM_SET(omega);
   if (m != n) err("wrong number of parameters!");
 }
 
@@ -92,7 +92,7 @@ double siir_proc_t::event_rates (double *rate, int n) const {
   RATE_CALC(params.psi2 * state.I2);
   RATE_CALC(params.sigma12 * state.I1);
   RATE_CALC(params.sigma21 * state.I2);
-  RATE_CALC(params.delta * state.R);
+  RATE_CALC(params.omega * state.R);
   if (m != n) err("wrong number of events!");
   return total;
 }
diff --git a/src/sir.cc b/src/sir.cc
index 7fd856f..0ff2d24 100644
--- a/src/sir.cc
+++ b/src/sir.cc
@@ -16,7 +16,7 @@ typedef struct {
   double Beta;
   double gamma;
   double psi;
-  double delta;
+  double omega;
   int S0;
   int I0;
   int R0;
@@ -32,7 +32,7 @@ std::string sir_proc_t::yaml (std::string tab) const {
     + YAML_PARAM(Beta)
     + YAML_PARAM(gamma)
     + YAML_PARAM(psi)
-    + YAML_PARAM(delta)
+    + YAML_PARAM(omega)
     + YAML_PARAM(S0)
     + YAML_PARAM(I0)
     + YAML_PARAM(R0);
@@ -50,7 +50,7 @@ void sir_proc_t::update_params (double *p, int n) {
   PARAM_SET(Beta);
   PARAM_SET(gamma);
   PARAM_SET(psi);
-  PARAM_SET(delta);
+  PARAM_SET(omega);
   if (m != n) err("wrong number of parameters!");
 }
 
@@ -70,7 +70,7 @@ double sir_proc_t::event_rates (double *rate, int n) const {
   RATE_CALC(params.Beta * state.S * state.I / state.N);
   RATE_CALC(params.gamma * state.I);
   RATE_CALC(params.psi * state.I);
-  RATE_CALC(params.delta * state.R);
+  RATE_CALC(params.omega * state.R);
   if (m != n) err("wrong number of events!");
   return total;
 }
diff --git a/src/sirs_pomp.c b/src/sirs_pomp.c
index 2acc30b..f48cc8e 100644
--- a/src/sirs_pomp.c
+++ b/src/sirs_pomp.c
@@ -5,7 +5,7 @@
 #define Beta      (__p[__parindex[0]])
 #define gamma     (__p[__parindex[1]])
 #define psi       (__p[__parindex[2]])
-#define Delta     (__p[__parindex[3]])
+#define omega     (__p[__parindex[3]])
 #define S0        (__p[__parindex[4]])
 #define I0        (__p[__parindex[5]])
 #define R0        (__p[__parindex[6]])
@@ -44,7 +44,7 @@ static double event_rates
   event_rate += (*rate = gamma*I);
   rate++;
   // loss of immunity
-  event_rate += (*rate = Delta*R);
+  event_rate += (*rate = omega*R);
   rate++;
   // sampling
   *penalty += psi*I;
@@ -150,7 +150,7 @@ void sirs_dmeas
 }
 
 #undef lik
-#undef Delta
+#undef omega
 #undef Beta
 #undef gamma
 #undef psi
diff --git a/tests/curtail.R b/tests/curtail.R
index f96afe6..bdf74ba 100644
--- a/tests/curtail.R
+++ b/tests/curtail.R
@@ -8,7 +8,7 @@ theme_set(theme_bw())
 set.seed(24963811)
 options(digits=3)
 
-runSEIR(time=5,S0=20,delta=2) -> x
+runSEIR(time=5,S0=20,omega=2) -> x
 
 plot_grid(
   x |>
diff --git a/tests/curtail.Rout.save b/tests/curtail.Rout.save
index 86bc096..659a686 100644
--- a/tests/curtail.Rout.save
+++ b/tests/curtail.Rout.save
@@ -27,7 +27,7 @@ Type 'q()' to quit R.
 > set.seed(24963811)
 > options(digits=3)
 > 
-> runSEIR(time=5,S0=20,delta=2) -> x
+> runSEIR(time=5,S0=20,omega=2) -> x
 > 
 > plot_grid(
 +   x |>
diff --git a/tests/diagram.R b/tests/diagram.R
index 9771487..0de6cc8 100644
--- a/tests/diagram.R
+++ b/tests/diagram.R
@@ -30,12 +30,12 @@ freeze(
 ) |> diagram(prune=FALSE,obscure=FALSE)
 dev.off()
 
-simulate("SIIR",time=0.3,sigma12=1,sigma21=0.1,delta=1) |>
+simulate("SIIR",time=0.3,sigma12=1,sigma21=0.1,omega=1) |>
   getInfo(description=TRUE) |>
   getElement("description") |>
   cat()
 
-simulate("SIIR",time=0.3,sigma12=0.1,sigma21=1,delta=1) |>
+simulate("SIIR",time=0.3,sigma12=0.1,sigma21=1,omega=1) |>
   getInfo(prune=FALSE,obscure=FALSE,description=TRUE) |>
   getElement("description") |>
   cat()
@@ -58,16 +58,16 @@ pal <- c("#00274c55","#ffcb0555","#00659755")
 
 png(filename="diagram-05.png",res=100,
   width=1000,height=190,units="px")
-freeze(simulate("SEIR",time=1,delta=1),seed=234551276) |>
+freeze(simulate("SEIR",time=1,omega=1),seed=234551276) |>
   diagram(obscure=FALSE,palette=pal)
 dev.off()
 
 try(
-  simulate("SEIR",time=2,delta=1) |>
+  simulate("SEIR",time=2,omega=1) |>
     diagram(obscure=FALSE,palette=pal[1])
 )
 
-simulate("SEIR",Beta=10,psi=2,sigma=3,time=1,delta=1) |>
+simulate("SEIR",Beta=10,psi=2,sigma=3,time=1,omega=1) |>
   freeze(seed=118551276) -> x
 
 png(filename="diagram-06.png",res=100,
diff --git a/tests/diagram.Rout.save b/tests/diagram.Rout.save
index d0df5c5..78d08d1 100644
--- a/tests/diagram.Rout.save
+++ b/tests/diagram.Rout.save
@@ -94,7 +94,7 @@ null device
 null device 
           1 
 > 
-> simulate("SIIR",time=0.3,sigma12=1,sigma21=0.1,delta=1) |>
+> simulate("SIIR",time=0.3,sigma12=1,sigma21=0.1,omega=1) |>
 +   getInfo(description=TRUE) |>
 +   getElement("description") |>
 +   cat()
@@ -107,7 +107,7 @@ node(30,0,0){blue(30,0)}, t = 0.074094
 node(42,0,1){blue(42,0)}, t = 0.161458
 node(61,0,2){blue(61,0)}, t = 0.240436
 > 
-> simulate("SIIR",time=0.3,sigma12=0.1,sigma21=1,delta=1) |>
+> simulate("SIIR",time=0.3,sigma12=0.1,sigma21=1,omega=1) |>
 +   getInfo(prune=FALSE,obscure=FALSE,description=TRUE) |>
 +   getElement("description") |>
 +   cat()
@@ -194,7 +194,7 @@ parameter:
   Beta: 2.000000
   gamma: 1.000000
   psi: 1.000000
-  delta: 0.000000
+  omega: 0.000000
   S0: 100
   I0: 2
   R0: 0
@@ -772,19 +772,19 @@ Error : cannot simulate backward! (current t=1, requested t=0.1)
 > 
 > png(filename="diagram-05.png",res=100,
 +   width=1000,height=190,units="px")
-> freeze(simulate("SEIR",time=1,delta=1),seed=234551276) |>
+> freeze(simulate("SEIR",time=1,omega=1),seed=234551276) |>
 +   diagram(obscure=FALSE,palette=pal)
 > dev.off()
 null device 
           1 
 > 
 > try(
-+   simulate("SEIR",time=2,delta=1) |>
++   simulate("SEIR",time=2,omega=1) |>
 +     diagram(obscure=FALSE,palette=pal[1])
 + )
 Error : in 'diagram': if specified as a vector, 'palette' must have length at least 2.
 > 
-> simulate("SEIR",Beta=10,psi=2,sigma=3,time=1,delta=1) |>
+> simulate("SEIR",Beta=10,psi=2,sigma=3,time=1,omega=1) |>
 +   freeze(seed=118551276) -> x
 > 
 > png(filename="diagram-06.png",res=100,
diff --git a/tests/seir1.R b/tests/seir1.R
index db54aa0..9d963d8 100644
--- a/tests/seir1.R
+++ b/tests/seir1.R
@@ -18,13 +18,13 @@ runSEIR(Beta=3,sigma=2,gamma=1,psi=2,S0=100,I0=5,time=1) |>
   simulate(time=100) |>
   plot(points=TRUE,time=NULL,obscure=FALSE)
 
-simulate("SEIR",delta=1,time=20,I0=4) -> x
+simulate("SEIR",omega=1,time=20,I0=4) -> x
 x |> yaml() -> y
 x |> lineages(obscure=FALSE) |> plot()
 
-simulate("SEIR",delta=1,time=2,I0=3) |>
+simulate("SEIR",omega=1,time=2,I0=3) |>
   diagram(obscure=FALSE,prune=TRUE)
 
-try(simulate("SEIR",delta=1,I0=-5,time=3))
+try(simulate("SEIR",omega=1,I0=-5,time=3))
 
 dev.off()
diff --git a/tests/seir1.Rout.save b/tests/seir1.Rout.save
index 423b728..8658444 100644
--- a/tests/seir1.Rout.save
+++ b/tests/seir1.Rout.save
@@ -38,14 +38,14 @@ Type 'q()' to quit R.
 +   simulate(time=100) |>
 +   plot(points=TRUE,time=NULL,obscure=FALSE)
 > 
-> simulate("SEIR",delta=1,time=20,I0=4) -> x
+> simulate("SEIR",omega=1,time=20,I0=4) -> x
 > x |> yaml() -> y
 > x |> lineages(obscure=FALSE) |> plot()
 > 
-> simulate("SEIR",delta=1,time=2,I0=3) |>
+> simulate("SEIR",omega=1,time=2,I0=3) |>
 +   diagram(obscure=FALSE,prune=TRUE)
 > 
-> try(simulate("SEIR",delta=1,I0=-5,time=3))
+> try(simulate("SEIR",omega=1,I0=-5,time=3))
 Error : in 'runSEIR': 'S0','E0','I0','R0' must be nonnegative integers.
 > 
 > dev.off()
diff --git a/tests/seir2.R b/tests/seir2.R
index 5f9fb87..5e35f4e 100644
--- a/tests/seir2.R
+++ b/tests/seir2.R
@@ -10,7 +10,7 @@ set.seed(842110120)
 options(digits=3)
 
 runSEIR(
-  Beta=4,sigma=1,gamma=1,psi=1,delta=1,
+  Beta=4,sigma=1,gamma=1,psi=1,omega=1,
   S0=100,E0=3,I0=5,R0=100,
   time=5
 ) -> G
@@ -25,7 +25,7 @@ G |>
 try(
   G |>
     seirs_pomp(
-      Beta=4,sigma=1,gamma=1,psi=1,delta=1,
+      Beta=4,sigma=1,gamma=1,psi=1,omega=1,
       S0=100,E0=3,I0=-5,R0=100
     ) -> po
 )
@@ -33,7 +33,7 @@ try(
 G |>
   curtail(time=3) |>
   seirs_pomp(
-    Beta=4,sigma=1,gamma=1,psi=1,delta=1,
+    Beta=4,sigma=1,gamma=1,psi=1,omega=1,
     S0=100,E0=3,I0=5,R0=100
   ) -> po
 
diff --git a/tests/seir2.Rout.save b/tests/seir2.Rout.save
index 9a7b114..469ba7a 100644
--- a/tests/seir2.Rout.save
+++ b/tests/seir2.Rout.save
@@ -29,7 +29,7 @@ Type 'q()' to quit R.
 > options(digits=3)
 > 
 > runSEIR(
-+   Beta=4,sigma=1,gamma=1,psi=1,delta=1,
++   Beta=4,sigma=1,gamma=1,psi=1,omega=1,
 +   S0=100,E0=3,I0=5,R0=100,
 +   time=5
 + ) -> G
@@ -44,7 +44,7 @@ Type 'q()' to quit R.
 > try(
 +   G |>
 +     seirs_pomp(
-+       Beta=4,sigma=1,gamma=1,psi=1,delta=1,
++       Beta=4,sigma=1,gamma=1,psi=1,omega=1,
 +       S0=100,E0=3,I0=-5,R0=100
 +     ) -> po
 + )
@@ -53,7 +53,7 @@ Error : in 'seirs_pomp': 'S0','E0','I0','R0' must be nonnegative integers.
 > G |>
 +   curtail(time=3) |>
 +   seirs_pomp(
-+     Beta=4,sigma=1,gamma=1,psi=1,delta=1,
++     Beta=4,sigma=1,gamma=1,psi=1,omega=1,
 +     S0=100,E0=3,I0=5,R0=100
 +   ) -> po
 NOTE: The provided objects 'genealogy','nsample' are available for use by POMP basic components.
diff --git a/tests/si2r.R b/tests/si2r.R
index c5e9003..ac42133 100644
--- a/tests/si2r.R
+++ b/tests/si2r.R
@@ -19,7 +19,7 @@ x |> plot(prune=FALSE,obscure=FALSE)
 x |> yaml() -> y
 x |> lineages(obscure=FALSE) |> plot()
 
-runSI2R(time=2,Beta=2,mu=3,gamma=1,psi1=2,psi2=2,delta=1) |>
+runSI2R(time=2,Beta=2,mu=3,gamma=1,psi1=2,psi2=2,omega=1) |>
   simulate(time=5) |>
   plot(prune=FALSE,obscure=FALSE,points=TRUE)
 
diff --git a/tests/si2r.Rout.save b/tests/si2r.Rout.save
index 1b30a96..9a2de22 100644
--- a/tests/si2r.Rout.save
+++ b/tests/si2r.Rout.save
@@ -39,7 +39,7 @@ Type 'q()' to quit R.
 > x |> yaml() -> y
 > x |> lineages(obscure=FALSE) |> plot()
 > 
-> runSI2R(time=2,Beta=2,mu=3,gamma=1,psi1=2,psi2=2,delta=1) |>
+> runSI2R(time=2,Beta=2,mu=3,gamma=1,psi1=2,psi2=2,omega=1) |>
 +   simulate(time=5) |>
 +   plot(prune=FALSE,obscure=FALSE,points=TRUE)
 > 
diff --git a/tests/sir1.R b/tests/sir1.R
index c8e0cb1..967a8b1 100644
--- a/tests/sir1.R
+++ b/tests/sir1.R
@@ -19,14 +19,14 @@ runSIR(Beta=3,gamma=1,psi=2,S0=100,I0=5,time=1) |>
   simulate(time=100) |>
   plot(points=TRUE,time=NULL)
 
-simulate("SIR",Beta=3,gamma=1,psi=2,delta=1,S0=100,I0=5,time=10) -> x
+simulate("SIR",Beta=3,gamma=1,psi=2,omega=1,S0=100,I0=5,time=10) -> x
 x |> yaml() -> y
 x |> lineages() |> plot()
 x |> geneal()
 
 x |>
   sir_pomp(
-    Beta=3,gamma=1,psi=2,delta=1,
+    Beta=3,gamma=1,psi=2,omega=1,
     S0=100,I0=5,R0=0
   ) |>
   pfilter(Np=5000) -> pf
@@ -38,7 +38,7 @@ try(runSIR(S0=-10,time=1))
 try(
   x |>
     sir_pomp(
-      Beta=3,gamma=1,psi=2,delta=1,
+      Beta=3,gamma=1,psi=2,omega=1,
       S0=-100,I0=5,R0=0
     )
 )
diff --git a/tests/sir1.Rout.save b/tests/sir1.Rout.save
index ab43502..fc20e66 100644
--- a/tests/sir1.Rout.save
+++ b/tests/sir1.Rout.save
@@ -39,7 +39,7 @@ Type 'q()' to quit R.
 +   simulate(time=100) |>
 +   plot(points=TRUE,time=NULL)
 > 
-> simulate("SIR",Beta=3,gamma=1,psi=2,delta=1,S0=100,I0=5,time=10) -> x
+> simulate("SIR",Beta=3,gamma=1,psi=2,omega=1,S0=100,I0=5,time=10) -> x
 > x |> yaml() -> y
 > x |> lineages() |> plot()
 > x |> geneal()
@@ -47,7 +47,7 @@ Type 'q()' to quit R.
 > 
 > x |>
 +   sir_pomp(
-+     Beta=3,gamma=1,psi=2,delta=1,
++     Beta=3,gamma=1,psi=2,omega=1,
 +     S0=100,I0=5,R0=0
 +   ) |>
 +   pfilter(Np=5000) -> pf
@@ -61,7 +61,7 @@ Error : in 'runSIR': 'S0','I0','R0' must be nonnegative integers.
 > try(
 +   x |>
 +     sir_pomp(
-+       Beta=3,gamma=1,psi=2,delta=1,
++       Beta=3,gamma=1,psi=2,omega=1,
 +       S0=-100,I0=5,R0=0
 +     )
 + )
diff --git a/yaml/R/seir.R b/yaml/R/seir.R
index d2c7e6d..7a0671d 100644
--- a/yaml/R/seir.R
+++ b/yaml/R/seir.R
@@ -9,7 +9,7 @@
 ##' @param sigma progression rate
 ##' @param gamma recovery rate
 ##' @param psi per capita sampling rate
-##' @param delta rate of waning of immunity
+##' @param omega rate of waning of immunity
 ##' @param S0 initial size of susceptible population
 ##' @param E0 initial size of exposed population
 ##' @param I0 initial size of infected population
@@ -23,9 +23,9 @@ NULL
 ##' @export
 runSEIR <- function (
   time, t0 = 0,
-  Beta = 4, sigma = 1, gamma = 1, psi = 1, delta = 0, S0 = 100, E0 = 5, I0 = 5, R0 = 0
+  Beta = 4, sigma = 1, gamma = 1, psi = 1, omega = 0, S0 = 100, E0 = 5, I0 = 5, R0 = 0
 ) {
-  params <- c(Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,delta=delta)
+  params <- c(Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,omega=omega)
   ivps <- c(S0=S0,E0=E0,I0=I0,R0=R0)
   x <- .Call(P_makeSEIR,params,ivps,t0)
   .Call(P_runSEIR,x,time) |>
@@ -36,10 +36,10 @@ runSEIR <- function (
 ##' @export
 continueSEIR <- function (
   object, time,
-  Beta = NA, sigma = NA, gamma = NA, psi = NA, delta = NA
+  Beta = NA, sigma = NA, gamma = NA, psi = NA, omega = NA
 ) {
   params <- c(
-    Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,delta=delta
+    Beta=Beta,sigma=sigma,gamma=gamma,psi=psi,omega=omega
   )
   x <- .Call(P_reviveSEIR,object,params)
   .Call(P_runSEIR,x,time) |>
diff --git a/yaml/R/si2r.R b/yaml/R/si2r.R
index 736737e..79e0650 100644
--- a/yaml/R/si2r.R
+++ b/yaml/R/si2r.R
@@ -8,7 +8,7 @@
 ##' @param Beta transmission rate
 ##' @param mu mean superspreading-event cluster size
 ##' @param gamma recovery rate
-##' @param delta rate of waning of immunity
+##' @param omega rate of waning of immunity
 ##' @param psi1 sampling rate for deme 1
 ##' @param psi2 sampling rate for deme 2
 ##' @param sigma12 rate of movement from deme 1 to deme 2
@@ -25,9 +25,9 @@ NULL
 ##' @export
 runSI2R <- function (
   time, t0 = 0,
-  Beta = 5, mu = 5, gamma = 1, delta = 0, psi1 = 1, psi2 = 0, sigma12 = 1, sigma21 = 3, S0 = 500, I0 = 10, R0 = 0
+  Beta = 5, mu = 5, gamma = 1, omega = 0, psi1 = 1, psi2 = 0, sigma12 = 1, sigma21 = 3, S0 = 500, I0 = 10, R0 = 0
 ) {
-  params <- c(Beta=Beta,mu=mu,gamma=gamma,delta=delta,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21)
+  params <- c(Beta=Beta,mu=mu,gamma=gamma,omega=omega,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21)
   ivps <- c(S0=S0,I0=I0,R0=R0)
   x <- .Call(P_makeSI2R,params,ivps,t0)
   .Call(P_runSI2R,x,time) |>
@@ -38,10 +38,10 @@ runSI2R <- function (
 ##' @export
 continueSI2R <- function (
   object, time,
-  Beta = NA, mu = NA, gamma = NA, delta = NA, psi1 = NA, psi2 = NA, sigma12 = NA, sigma21 = NA
+  Beta = NA, mu = NA, gamma = NA, omega = NA, psi1 = NA, psi2 = NA, sigma12 = NA, sigma21 = NA
 ) {
   params <- c(
-    Beta=Beta,mu=mu,gamma=gamma,delta=delta,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21
+    Beta=Beta,mu=mu,gamma=gamma,omega=omega,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21
   )
   x <- .Call(P_reviveSI2R,object,params)
   .Call(P_runSI2R,x,time) |>
diff --git a/yaml/R/siir.R b/yaml/R/siir.R
index 46c4250..71aabf7 100644
--- a/yaml/R/siir.R
+++ b/yaml/R/siir.R
@@ -12,7 +12,7 @@
 ##' @param psi2 sampling rate for deme 2
 ##' @param sigma12 rate of movement from deme 1 to deme 2
 ##' @param sigma21 rate of movement from deme 2 to deme 1
-##' @param delta rate of loss of immunity
+##' @param omega rate of loss of immunity
 ##' @param S0 initial size of susceptible population
 ##' @param I1_0 initial size of deme-1 infected population
 ##' @param I2_0 initial size of deme-2 infected population
@@ -26,9 +26,9 @@ NULL
 ##' @export
 runSIIR <- function (
   time, t0 = 0,
-  Beta1 = 5, Beta2 = 5, gamma = 1, psi1 = 1, psi2 = 0, sigma12 = 0, sigma21 = 0, delta = 0, S0 = 500, I1_0 = 10, I2_0 = 10, R0 = 0
+  Beta1 = 5, Beta2 = 5, gamma = 1, psi1 = 1, psi2 = 0, sigma12 = 0, sigma21 = 0, omega = 0, S0 = 500, I1_0 = 10, I2_0 = 10, R0 = 0
 ) {
-  params <- c(Beta1=Beta1,Beta2=Beta2,gamma=gamma,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21,delta=delta)
+  params <- c(Beta1=Beta1,Beta2=Beta2,gamma=gamma,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21,omega=omega)
   ivps <- c(S0=S0,I1_0=I1_0,I2_0=I2_0,R0=R0)
   x <- .Call(P_makeSIIR,params,ivps,t0)
   .Call(P_runSIIR,x,time) |>
@@ -39,10 +39,10 @@ runSIIR <- function (
 ##' @export
 continueSIIR <- function (
   object, time,
-  Beta1 = NA, Beta2 = NA, gamma = NA, psi1 = NA, psi2 = NA, sigma12 = NA, sigma21 = NA, delta = NA
+  Beta1 = NA, Beta2 = NA, gamma = NA, psi1 = NA, psi2 = NA, sigma12 = NA, sigma21 = NA, omega = NA
 ) {
   params <- c(
-    Beta1=Beta1,Beta2=Beta2,gamma=gamma,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21,delta=delta
+    Beta1=Beta1,Beta2=Beta2,gamma=gamma,psi1=psi1,psi2=psi2,sigma12=sigma12,sigma21=sigma21,omega=omega
   )
   x <- .Call(P_reviveSIIR,object,params)
   .Call(P_runSIIR,x,time) |>
diff --git a/yaml/R/sir.R b/yaml/R/sir.R
index 3fcde0d..10d7a38 100644
--- a/yaml/R/sir.R
+++ b/yaml/R/sir.R
@@ -8,7 +8,7 @@
 ##' @param Beta transmission rate
 ##' @param gamma recovery rate
 ##' @param psi per capita sampling rate
-##' @param delta rate of waning of immunity
+##' @param omega rate of waning of immunity
 ##' @param S0 initial size of susceptible population
 ##' @param I0 initial size of infected population
 ##' @param R0 initial size of immune population
@@ -21,9 +21,9 @@ NULL
 ##' @export
 runSIR <- function (
   time, t0 = 0,
-  Beta = 4, gamma = 1, psi = 1, delta = 0, S0 = 100, I0 = 5, R0 = 0
+  Beta = 4, gamma = 1, psi = 1, omega = 0, S0 = 100, I0 = 5, R0 = 0
 ) {
-  params <- c(Beta=Beta,gamma=gamma,psi=psi,delta=delta)
+  params <- c(Beta=Beta,gamma=gamma,psi=psi,omega=omega)
   ivps <- c(S0=S0,I0=I0,R0=R0)
   x <- .Call(P_makeSIR,params,ivps,t0)
   .Call(P_runSIR,x,time) |>
@@ -34,10 +34,10 @@ runSIR <- function (
 ##' @export
 continueSIR <- function (
   object, time,
-  Beta = NA, gamma = NA, psi = NA, delta = NA
+  Beta = NA, gamma = NA, psi = NA, omega = NA
 ) {
   params <- c(
-    Beta=Beta,gamma=gamma,psi=psi,delta=delta
+    Beta=Beta,gamma=gamma,psi=psi,omega=omega
   )
   x <- .Call(P_reviveSIR,object,params)
   .Call(P_runSIR,x,time) |>
diff --git a/yaml/seir.yml b/yaml/seir.yml
index bff729f..b8ab03a 100644
--- a/yaml/seir.yml
+++ b/yaml/seir.yml
@@ -24,8 +24,8 @@ parameter:
     description: per capita sampling rate
     default: 1
     type: double
-  delta:
-    name: delta
+  omega:
+    name: omega
     description: rate of waning of immunity
     default: 0
     type: double
@@ -89,4 +89,4 @@ events:
     jump: sample(1);
   waning:
     jump: state.R -= 1; state.S += 1;
-    rate: params.delta * state.R
+    rate: params.omega * state.R
diff --git a/yaml/si2r.yml b/yaml/si2r.yml
index ddb2900..c098b05 100644
--- a/yaml/si2r.yml
+++ b/yaml/si2r.yml
@@ -19,8 +19,8 @@ parameter:
     description: recovery rate
     type: double
     default: 1
-  delta:
-    name: delta
+  omega:
+    name: omega
     description: rate of waning of immunity
     default: 0
     type: double
@@ -118,4 +118,4 @@ events:
     rate: params.sigma21 * state.I2
   waning:
     jump: state.R -= 1; state.S += 1;
-    rate: params.delta * state.R
+    rate: params.omega * state.R
diff --git a/yaml/siir.yml b/yaml/siir.yml
index d4e6540..dc730b4 100644
--- a/yaml/siir.yml
+++ b/yaml/siir.yml
@@ -39,8 +39,8 @@ parameter:
     description: rate of movement from deme 2 to deme 1
     default: 0
     type: double
-  delta:
-    name: delta
+  omega:
+    name: omega
     description: rate of loss of immunity
     default: 0
     type: double
@@ -116,4 +116,4 @@ events:
     rate: params.sigma21 * state.I2
   wane:
     jump: state.S += 1; state.R -= 1;
-    rate: params.delta * state.R
+    rate: params.omega * state.R
diff --git a/yaml/sir.yml b/yaml/sir.yml
index 55ce7da..e654743 100644
--- a/yaml/sir.yml
+++ b/yaml/sir.yml
@@ -19,8 +19,8 @@ parameter:
     description: per capita sampling rate
     default: 1
     type: double
-  delta:
-    name: delta
+  omega:
+    name: omega
     description: rate of waning of immunity
     default: 0
     type: double
@@ -71,4 +71,4 @@ events:
     jump: sample();
   waning:
     jump: state.R -= 1; state.S += 1;
-    rate: params.delta * state.R
+    rate: params.omega * state.R
diff --git a/yaml/src/seir.cc b/yaml/src/seir.cc
index 1d81382..5ff0f72 100644
--- a/yaml/src/seir.cc
+++ b/yaml/src/seir.cc
@@ -18,7 +18,7 @@ typedef struct {
   double sigma;
   double gamma;
   double psi;
-  double delta;
+  double omega;
   int S0;
   int E0;
   int I0;
@@ -36,7 +36,7 @@ std::string seir_proc_t::yaml (std::string tab) const {
     + YAML_PARAM(sigma)
     + YAML_PARAM(gamma)
     + YAML_PARAM(psi)
-    + YAML_PARAM(delta)
+    + YAML_PARAM(omega)
     + YAML_PARAM(S0)
     + YAML_PARAM(E0)
     + YAML_PARAM(I0)
@@ -57,7 +57,7 @@ void seir_proc_t::update_params (double *p, int n) {
   PARAM_SET(sigma);
   PARAM_SET(gamma);
   PARAM_SET(psi);
-  PARAM_SET(delta);
+  PARAM_SET(omega);
   if (m != n) err("wrong number of parameters!");
 }
 
@@ -79,7 +79,7 @@ double seir_proc_t::event_rates (double *rate, int n) const {
   RATE_CALC(params.sigma * state.E);
   RATE_CALC(params.gamma * state.I);
   RATE_CALC(params.psi * state.I);
-  RATE_CALC(params.delta * state.R);
+  RATE_CALC(params.omega * state.R);
   if (m != n) err("wrong number of events!");
   return total;
 }
diff --git a/yaml/src/si2r.cc b/yaml/src/si2r.cc
index db758a1..4bfda79 100644
--- a/yaml/src/si2r.cc
+++ b/yaml/src/si2r.cc
@@ -17,7 +17,7 @@ typedef struct {
   double Beta;
   double mu;
   double gamma;
-  double delta;
+  double omega;
   double psi1;
   double psi2;
   double sigma12;
@@ -37,7 +37,7 @@ std::string si2r_proc_t::yaml (std::string tab) const {
     + YAML_PARAM(Beta)
     + YAML_PARAM(mu)
     + YAML_PARAM(gamma)
-    + YAML_PARAM(delta)
+    + YAML_PARAM(omega)
     + YAML_PARAM(psi1)
     + YAML_PARAM(psi2)
     + YAML_PARAM(sigma12)
@@ -60,7 +60,7 @@ void si2r_proc_t::update_params (double *p, int n) {
   PARAM_SET(Beta);
   PARAM_SET(mu);
   PARAM_SET(gamma);
-  PARAM_SET(delta);
+  PARAM_SET(omega);
   PARAM_SET(psi1);
   PARAM_SET(psi2);
   PARAM_SET(sigma12);
@@ -89,7 +89,7 @@ double si2r_proc_t::event_rates (double *rate, int n) const {
   RATE_CALC(params.psi2 * state.I2);
   RATE_CALC(params.sigma12 * state.I1);
   RATE_CALC(params.sigma21 * state.I2);
-  RATE_CALC(params.delta * state.R);
+  RATE_CALC(params.omega * state.R);
   if (m != n) err("wrong number of events!");
   return total;
 }
diff --git a/yaml/src/siir.cc b/yaml/src/siir.cc
index 946ee91..298b8e8 100644
--- a/yaml/src/siir.cc
+++ b/yaml/src/siir.cc
@@ -21,7 +21,7 @@ typedef struct {
   double psi2;
   double sigma12;
   double sigma21;
-  double delta;
+  double omega;
   int S0;
   int I1_0;
   int I2_0;
@@ -42,7 +42,7 @@ std::string siir_proc_t::yaml (std::string tab) const {
     + YAML_PARAM(psi2)
     + YAML_PARAM(sigma12)
     + YAML_PARAM(sigma21)
-    + YAML_PARAM(delta)
+    + YAML_PARAM(omega)
     + YAML_PARAM(S0)
     + YAML_PARAM(I1_0)
     + YAML_PARAM(I2_0)
@@ -66,7 +66,7 @@ void siir_proc_t::update_params (double *p, int n) {
   PARAM_SET(psi2);
   PARAM_SET(sigma12);
   PARAM_SET(sigma21);
-  PARAM_SET(delta);
+  PARAM_SET(omega);
   if (m != n) err("wrong number of parameters!");
 }
 
@@ -92,7 +92,7 @@ double siir_proc_t::event_rates (double *rate, int n) const {
   RATE_CALC(params.psi2 * state.I2);
   RATE_CALC(params.sigma12 * state.I1);
   RATE_CALC(params.sigma21 * state.I2);
-  RATE_CALC(params.delta * state.R);
+  RATE_CALC(params.omega * state.R);
   if (m != n) err("wrong number of events!");
   return total;
 }
diff --git a/yaml/src/sir.cc b/yaml/src/sir.cc
index ed5f1de..8f3ae12 100644
--- a/yaml/src/sir.cc
+++ b/yaml/src/sir.cc
@@ -16,7 +16,7 @@ typedef struct {
   double Beta;
   double gamma;
   double psi;
-  double delta;
+  double omega;
   int S0;
   int I0;
   int R0;
@@ -32,7 +32,7 @@ std::string sir_proc_t::yaml (std::string tab) const {
     + YAML_PARAM(Beta)
     + YAML_PARAM(gamma)
     + YAML_PARAM(psi)
-    + YAML_PARAM(delta)
+    + YAML_PARAM(omega)
     + YAML_PARAM(S0)
     + YAML_PARAM(I0)
     + YAML_PARAM(R0);
@@ -50,7 +50,7 @@ void sir_proc_t::update_params (double *p, int n) {
   PARAM_SET(Beta);
   PARAM_SET(gamma);
   PARAM_SET(psi);
-  PARAM_SET(delta);
+  PARAM_SET(omega);
   if (m != n) err("wrong number of parameters!");
 }
 
@@ -70,7 +70,7 @@ double sir_proc_t::event_rates (double *rate, int n) const {
   RATE_CALC(params.Beta * state.S * state.I / state.N);
   RATE_CALC(params.gamma * state.I);
   RATE_CALC(params.psi * state.I);
-  RATE_CALC(params.delta * state.R);
+  RATE_CALC(params.omega * state.R);
   if (m != n) err("wrong number of events!");
   return total;
 }